The disclosed subject matter provides techniques for detection of minimal residual disease (MRD), such as in multiple myeloma. Multiple myeloma (MM) accounts for approximately 1.3% of all types of cancer. Certain drug regimen and stem-cell transplantation have improved survival, with a current three-year survival rate at 56.6%. A goal of treatment is to obtain complete response (CR), defined as the absence of monoclonal protein by immunofixation and less than 5% plasma cells in bone marrow (BM). Of patients who obtain CR, those who are negative in minimal residual disease (MRD) in their bone marrow by flow cytometry have better survival than those who are MRD positive. Identification and measurement of MRD can be used in MM care for selecting and guiding therapeutic strategies.
Methods for MRD detection can be based on evaluation of plasma cells obtained from bone marrow aspirates, including multiparameter flow cytometry (MFC) that can detect one clonal cell in 104 normal cells, allele specific polymerase chain reaction (ASO-PCR) that involves sequencing the rearranged variable region (VDJ), and deep sequencing that amplifies RNA with locus-specific primers followed by sequencing. Limitations can include, for example, the poor survival of plasma cells in the specimen that can cause failure of MRD detection, and/or the invasiveness of the procedure that prohibits frequent monitoring.
Methods that are sensitive, specific, non-invasive, and amenable to standardization can be of interest for MRD detection. Serum-based methods can be used, but certain protein electrophoresis (SPEP), immunofixation (IFE) and free light chain ratio (FLC) techniques can be low in sensitivity with limits of detection (LOD) of 500-2000 mg/L (SPEP), 100-150 mg/L (IFE) and up to 1 mg/L (FLC), respectively. Aptamers, single-strand oligonucleotides (oligomers) that bind to targets with high specificity and affinity, can be attractive receptors capable of allowing highly sensitive assays. Certain aptamers have been used to detect proteins in serum, including immunoglobulins with LOD below 2.5 μg/L. These sensitivities are orders of magnitude higher than those of certain serum-based M-Ig detection methods such as SPEP, IFE and FLC.
Apatamers can be obtained from randomized oligomer libraries via an in vitro process termed systematic evolution of ligands by exponential enrichment (SELEX). Since aptamers are isolated from randomized oligomer libraries through an in vitro process termed systematic evolution of ligands by exponential enrichment (SELEX), they can be advantageous over antibodies for analyte detection because they: (1) can be synthetically developed (rather than via immunization of animals) for a target, (2) are amenable to rapid manufacture with minimal batch-to-batch variability, (3) offer controlled selectivity by removing oligomers that bind to counter targets (counter selection) and that nonspecifically bind to the target support (negative selection), and (4) can be designed to bind to particular functional domains of a target (to differentiate targets that differ only minimally) and to possess environmental (e.g., temperature or pH) responsive-ness (for use in sensitive assays).